TODO: not linked anywhere, maybe just delete it

How do I ...¶

... calculate SEDs directly with ProDiMo?¶

see ProDiMo_SED

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... calculate gas emission line profiles and line fluxes directly with ProDiMo?¶

see ProDiMo_Line_Transfer

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... use a fixed density structure of the disk?¶

see fixed_density_structure and 1Dinterface

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... run a model with time-dependent disk chemistry?¶

see How_to_run_a_time_dependent_chemistry_model

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... run a X-ray model?¶

see How_to_run_a_X-ray_model

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... switch on detailed PAH heating/cooling and PAH chemistry?¶

see PAH_heating_and_chemistry

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... control the way that ProDiMo calculates the photorates?¶

see UV_photorates

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... run a ProDiMo-model with dust settling¶

see dust_settling

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... see what's going on in the chemistry¶

ProDiMo writes more output and waits for interactive commands if you increase verbose_level in Parameter.in. Even better, leave verbose_level=0 there, but change chemistry_and_energybalance.f and uncomment a line like

 if ((ix.eq.11).and.(iz.eq.10)) verbose=1

which tells ProDiMo to increase verbose_level once a certain grid point is reached. The meaning of verbose is ...

 verbose = -1   : no wait, only very little warnings
 verbose = 0    : no wait, standard warnings
 verbose = 1    : wait for return (or other command) after finishing one grid point
 verbose = 2    : wait after every Newton-Raphson chemistry step
 verbose = 3    : (can't remember)
 verbose = 4    : check analytic against numerical chemical Jacobian

Now, if ProDiMo waits for input (verbose>0) you can just press to go to the next point. Or, you can give one of these commands

 ENTER      : next point
 0...4      : change verbose level
 Q          : search for thermal bifurcations
 character  : go to chemical analysis

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... analyze the chemistry¶

If ProDiMo waits for input (verbose>0) and you type a character, you are prompted for the name of a species for chemical analysis. Type 'q' if you want to return without analysis

 input species to analyse ...
> H2O
  gas temperature =   980.861597112949
 H nuclei density =   1885537853.20952
              chi =   112260.313525271
 formation ... H2O
   27    55 NN: H2     + OH       --> H2O    + H     2.11E-12 1.06E-06
  918 10044 PH: H3O+   + PHOTON   --> H2O    + H+    1.65E-02 8.64E-08
 destruction ... H2O
  806  4205 PH: H2O    + PHOTON   --> OH     + H     1.80E+00 1.16E-06
  915 10040 P3: H2O    + PHOTON   --> O      + H2    6.40E-03 4.11E-09
 particle density = 6.426E-07 concentration = 3.408E-16
 total rate = 1.275E-22
 input species to analyse ...
> q

particle density is in [1/cm^{3], concentration means nmol/n, total rate is the sum of all rates [1/cm}3/s], should be zero. The meaning of the reaction entries are as

   27       55      NN:    H2 + OH --> H2O + H    2.11E-12    1.06E-06
  ^^^^     ^^^^    ^^^^                           ^^^^^^^^    ^^^^^^^^
 running   number  type    reaction              rate coeff     rate
 reaction  in                                    [depends]    [1/cm^3/s]
 number    UMIST

The rate is the rate coefficient multiplied by the particle densities of the reactants, except for ice desorption, which is more difficult.

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... search for thermal bifurcations¶

If you press "Q" instead, ProDiMo varies the Tgas systematically between 20K and 10000K, calls the chemistry, calculates the net heating function Q(Tgas) and lists the results, before going to the next grid point. For thermal stability Q(Teq)=0 and Q'(Teq)<0 at the equilibrium gas temperature Teq=Tgas(Q=0). It is possible that there exists more than one root of Q(Tgas)=0, a physical non-uniqueness of the condition of gas energy balance, sometimes referred to as "thermal bifurcations". You can manually search for these bifurcations this way.

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